Spinal cord data

Morphometry

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np

import pandas as pd
pd.set_option('display.max_rows', None)
pd.set_option('display.max_columns', None)
pd.set_option('display.width', 1000)
pd.set_option('display.colheader_justify', 'center')
pd.set_option('display.precision', 3)

# Import custom tools
from tools.data import Data
from tools.plot import Plot
from tools.stats import Stats

Download data

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

--2022-09-13 12:55:04--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20220804/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.112.4
Connecting to github.com (github.com)|140.82.112.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220913T125504Z&X-Amz-Expires=300&X-Amz-Signature=7231f086da7ab6e6be4d5ac1abb37119aef176d391aae2b807711a8e9cd3bd85&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-09-13 12:55:04--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220913T125504Z&X-Amz-Expires=300&X-Amz-Signature=7231f086da7ab6e6be4d5ac1abb37119aef176d391aae2b807711a8e9cd3bd85&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 47607 (46K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... .......... .......... .......... ......    100% 9.38M=0.005s

2022-09-13 12:55:04 (9.38 MB/s) - ‘spinalcord_results.zip’ saved [47607/47607]

Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/T1.csv       

Load data plot it

dataset.num_sessions

dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-wm')

fig_spine.title = 'WM spinal cord morphometry'

White matter

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-wm')

Grey matter

fig_spine = Plot(dataset, plot_name = 'spine-gm')

fig_spine.title = 'GM spinal cord morphometry'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-gm')

Statistics

stats_csa = Stats(dataset)
stats_csa.build_df()
stats_csa.build_stats_table()
display(stats_csa.stats_table)

	WM area (T1w)	WM area (T2w)	GM area (T2w)
intrasubject CoV mean	0.045	0.023	0.103
intrasubject CoV std	0.033	0.017	0.104
intersubject mean CoV	0.051	0.097	0.047

Quantitative MRI

White matter

data_type = 'qmri'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Archive:  spinalcord_results.zip
  inflating: data/qmri/DWI_RD.csv    
  inflating: data/qmri/DWI_FA.csv    
  inflating: data/qmri/csa-SC_T2w.csv  
  inflating: data/qmri/DWI_MD.csv    
  inflating: data/qmri/MTR.csv       
  inflating: data/qmri/MTsat.csv     
  inflating: data/qmri/csa-GM_T2s.csv  
  inflating: data/qmri/csa-SC_T1w.csv  
  inflating: data/qmri/T1.csv        

--2022-09-13 12:55:05--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20220804/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.112.4
Connecting to github.com (github.com)|140.82.112.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220913T125505Z&X-Amz-Expires=300&X-Amz-Signature=7d19f8bdca68edc66aab92f5542b3d0c979ef517919904fb0b8c535a0a8169cf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-09-13 12:55:05--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220913%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220913T125505Z&X-Amz-Expires=300&X-Amz-Signature=7d19f8bdca68edc66aab92f5542b3d0c979ef517919904fb0b8c535a0a8169cf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 47607 (46K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... .......... .......... .......... ......    100% 9.60M=0.005s

2022-09-13 12:55:05 (9.60 MB/s) - ‘spinalcord_results.zip’ saved [47607/47607]

dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord qMRI measures'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-qmri-wm')

Statistics

stats_qmri = Stats(dataset)
stats_qmri.build_df()
stats_qmri.build_stats_table()
display(stats_qmri.stats_table)

	FA (DWI)	MD (DWI)	RD (DWI)	MTR	MTsat	T1 (MTsat)
intrasubject CoV mean	0.081	0.099	0.112	0.051	0.079	0.064
intrasubject CoV std	0.052	0.065	0.032	0.052	0.049	0.035
intersubject mean CoV	0.046	0.043	0.082	0.046	0.04	0.079